The merger values each Just Eat share at 916p after Takeaway.com jacked up its original offer price of around 704p per share.
The merged company, which will be led by Takeaway chief executive Jitse Groen, will have its headquarters in Amsterdam and a listing in London. However, these offers were rejected by Just Eat's shareholders.
Online food ordering company Takeaway.com has won the battle for the UK-listed Just Eat with a £5.9bn all-share offer.
The takeover, which will create one of the world's largest takeaway delivery companies, valued Just Eat at 889p per share taking its market value to around £5.9 billion.
Van Dijk said Prosus would remain disciplined in how it allocates its capital and the price that it would offers for such transactions in future.
The Dutch firm announced an all-stock bid for Just Eat in late July valuing the British company at about 731 pence per share, or 5bn pounds.
The combination of the two firms will create a delivery service worth around nine billion pounds ($11 billion) capable of competing against Britain-based Deliveroo and Uber Eats of the United States.
On Thursday, Takeaway.com said its shareholders had approved the Just Eat merger at an extraordinary general meeting.
Takeaway says the combination will achieve annual cost savings of about 20 million euros from centralising orders on its platform, unifying brands and improving procurement.
That plan was upended when Prosus laid down the first of three unsolicited rival bids in October.
Prosus had argued it has the resources to make the significant investments in Just Eat necessary for it to stay competitive. In recent years it has acquired Berlin-based food ordering startup Lieferando and Delivery Hero's German food delivery businesses Lieferheld, Pizza.de and foodora.
Shareholder approval ends a bidding war between the Dutch firm and Prosus, an investment group backed by South African e-commerce giant Naspers, which had made a final cash offer of 800p per share shortly before Takeaway.com swooped with its knockout blow.